Variant report

Variant	rs58634778
Chromosome Location	chr1:113155161-113155162
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113155147-113155177	K562	blood:	n/a	n/a
2	POLR2A	chr1:113155160-113155194	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:113008046..113009609-chr1:113154627..113156766,2	MCF-7	breast:
2	chr1:113044938..113047798-chr1:113154347..113157279,3	MCF-7	breast:
3	chr1:113143142..113146468-chr1:113154015..113156949,3	MCF-7	breast:

Variant related genes	Relation type
ST7L	TF binding region
ENSG00000134245	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10399919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102490	0.90[AFR][1000 genomes]
rs11102500	0.90[AFR][1000 genomes]
rs11102519	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102521	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060267	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069022	0.85[AFR][1000 genomes]
rs12069740	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12073750	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074157	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077330	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080006	0.90[AFR][1000 genomes]
rs12082350	0.83[AFR][1000 genomes]
rs12087862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091635	0.90[AFR][1000 genomes]
rs12094504	0.85[AFR][1000 genomes]
rs12095563	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030446	0.83[AFR][1000 genomes]
rs17030451	0.83[AFR][1000 genomes]
rs17030455	0.85[AFR][1000 genomes]
rs17030475	0.90[AFR][1000 genomes]
rs17030592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4424506	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57573777	1.00[AMR][1000 genomes]
rs59053530	1.00[AMR][1000 genomes]
rs59324334	0.85[AFR][1000 genomes]
rs61203550	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984509	1.00[AMR][1000 genomes]
rs72984515	1.00[AMR][1000 genomes]
rs72986505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72986535	1.00[AMR][1000 genomes]
rs72993072	0.90[AFR][1000 genomes]
rs9919308	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113109000-113160000	Weak transcription	Gastric	stomach
2	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
3	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
4	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
8	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
10	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
19	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:113140200-113159200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:113140400-113160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr1:113140600-113159200	Strong transcription	Fetal Stomach	stomach
23	chr1:113144000-113158600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:113144000-113160800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:113145000-113159600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr1:113145800-113159400	Strong transcription	Fetal Muscle Trunk	muscle
27	chr1:113146200-113156000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:113146800-113159000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:113147800-113158400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr1:113148200-113156600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:113148200-113156800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr1:113148200-113156800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:113148200-113158400	Strong transcription	Brain Germinal Matrix	brain
34	chr1:113148200-113158800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:113148200-113158800	Strong transcription	Liver	Liver
36	chr1:113148200-113158800	Strong transcription	Dnd41	blood
37	chr1:113148200-113159000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:113148200-113159000	Strong transcription	Placenta	Placenta
39	chr1:113148200-113159200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:113148200-113159800	Strong transcription	Fetal Intestine Small	intestine
41	chr1:113148400-113156800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:113148400-113157000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr1:113148400-113158600	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr1:113148400-113158600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:113148400-113158800	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr1:113148400-113158800	Strong transcription	Adipose Nuclei	Adipose
47	chr1:113148400-113158800	Strong transcription	Osteobl	bone
48	chr1:113148400-113159000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:113148400-113159200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr1:113148400-113159200	Strong transcription	Fetal Brain Female	brain

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